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Fix bug with variant metrics not being added to top of MultiQC report #224

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merged 3 commits into from
Jul 22, 2021
Merged

Fix bug with variant metrics not being added to top of MultiQC report #224

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733eec2
Fix file pattern regex in JSON schema
drpatelh Jul 21, 2021
8bdbe57
Replace commas with semi-colon in summary metrics
drpatelh Jul 21, 2021
17829fa
Convert variable to string
drpatelh Jul 22, 2021
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4 changes: 2 additions & 2 deletions bin/multiqc_to_custom_csv.py
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Original file line number Diff line number Diff line change
Expand Up @@ -159,12 +159,12 @@ def metrics_dict_to_file(
for field in field_list:
if field in metrics_dict[k]:
if metrics_dict[k][field]:
row_list.append(metrics_dict[k][field])
row_list.append(str(metrics_dict[k][field]).replace(',', ';'))
else:
row_list.append("NA")
else:
row_list.append("NA")
fout.write("{}\n".format(",".join(map(str, row_list))))
fout.write("{}\n".format(",".join(row_list)))
fout.close()
return metrics_dict

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12 changes: 6 additions & 6 deletions nextflow_schema.json
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@
"type": "string",
"format": "file-path",
"mimetype": "text/csv",
"pattern": "\\.csv$",
"pattern": "^\\S+\\.csv$",
"schema": "assets/schema_input.json",
"fa_icon": "fas fa-file-csv",
"help_text": "You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/viralrecon/docs/usage#introduction).",
Expand Down Expand Up @@ -63,7 +63,7 @@
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "\\.fn?a(sta)?(\\.gz)?$",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"fa_icon": "fas fa-font",
"description": "Path to FASTA genome file.",
"help_text": "If you have no genome reference available, the pipeline can build one using a FASTA file. This requires additional time and resources, so it's better to use a pre-build index if possible."
Expand All @@ -72,7 +72,7 @@
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "\\.gff(\\.gz)?$",
"pattern": "^\\S+\\.gff(\\.gz)?$",
"description": "Full path to GFF annotation file.",
"fa_icon": "fas fa-file-invoice"
},
Expand All @@ -86,7 +86,7 @@
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "\\.bed(\\.gz)?$",
"pattern": "^\\S+\\.bed(\\.gz)?$",
"description": "If the '--protocol amplicon' parameter is provided then iVar is used to trim primer sequences after read alignment and before variant calling.",
"help_text": "iVar uses the primer positions relative to the viral genome supplied in this file to soft clip primer sequences from a coordinate sorted BAM file. The file must be in BED format as highlighted below:\n\n```\nMN908947.3 30 54 nCoV-2019_1_LEFT 60 -\nMN908947.3 385 410 nCoV-2019_1_RIGHT 60 +\nMN908947.3 320 342 nCoV-2019_2_LEFT 60 -\nMN908947.3 704 726 nCoV-2019_2_RIGHT 60 +\n```",
"fa_icon": "fas fa-stream"
Expand All @@ -95,7 +95,7 @@
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "\\.fn?a(sta)?(\\.gz)?$",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"description": "If the '--protocol amplicon' parameter is provided then Cutadapt is used to trim primer sequences from FastQ files before de novo assembly.",
"help_text": "This file must contain amplicon primer sequences in Fasta format. An example is shown below:\n\n```\n>nCoV-2019_1_LEFT\nACCAACCAACTTTCGATCTCTTGT\n>nCoV-2019_1_RIGHT\nCATCTTTAAGATGTTGACGTGCCTC\n>nCoV-2019_2_LEFT\nCTGTTTTACAGGTTCGCGACGT\n>nCoV-2019_2_RIGHT\nTAAGGATCAGTGCCAAGCTCGT\n```",
"fa_icon": "fas fa-stream"
Expand Down Expand Up @@ -156,7 +156,7 @@
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "\\.txt$",
"pattern": "^\\S+\\.txt$",
"description": "Sequencing summary file generated after Nanopore run completion.",
"help_text": " e.g. '--sequencing_summary ./20191023_1522_MC-110615_0_FAO93606_12bf9b4f/sequencing_summary.txt'. Not required when running the pipeline with the '--artic_minion_caller medaka' workflow.",
"fa_icon": "fas fa-file"
Expand Down